The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_005633.3(SOS1):c.508A>G (p.Lys170Glu)

CA235342

40651 (ClinVar)

Gene: SOS1
Condition: Noonan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 07b0e3e7-5c67-41c3-a988-3c438dfba738
Approved on: 2017-04-03
Published on: 2018-12-10

HGVS expressions

NM_005633.3:c.508A>G
NM_005633.3(SOS1):c.508A>G (p.Lys170Glu)
NC_000002.12:g.39056704T>C
CM000664.2:g.39056704T>C
NC_000002.11:g.39283845T>C
CM000664.1:g.39283845T>C
NC_000002.10:g.39137349T>C
NG_007530.1:g.68760A>G
ENST00000395038.6:c.508A>G
ENST00000402219.6:c.508A>G
ENST00000426016.5:c.508A>G
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Pathogenic

Met criteria codes 6
PM1 PM6 PM2 PS3 PP3 PP2

Evidence Links 5

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.508A>G (p.Lys170Glu) variant in SOS1 has been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6; PMID 19020799, 21387466). In vitro functional studies provide some evidence that the p.Lys170Glu variant may impact protein function (PS3; PMID 21784453, 23487764). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the SOS1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of SOS1 (PM1; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Lys170Glu variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PP2, PP3, PM1, PM2, PM6, PS3.
Met criteria codes
PM1
Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of SOS1 (PM1; PMID 29493581)

PM6
The c.508A>G (p.Lys170Glu) variant in SOS1 has been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6; PMID 19020799, 21387466)

PM2
This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org).
PS3
In vitro functional studies provide some evidence that the p.Lys170Glu variant may impact protein function (PS3; PMID 21784453, 23487764).

PP3
Computational prediction tools and conservation analysis suggest that the p.Lys170Glu variant may impact the protein (PP3).
PP2
The variant is in SOS1, which has been defined by the ClinGen RASopathy Expert Panel as a gene with low rate of benign missense with missense variants commonly being pathogenic (PP2; PMID 29493581).
Curation History
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